I'm using the linked sprite collection functionality (again, awesome). For the output atlas that gets generated I have set it to be a normal map, grayscale, and enabled mipmaps. I've attached an image that shows the settings.
I then go and rebuild the atlases by clicking "commit" in the sprite collection editor. This does everything great, but the mip map setting on the atlas for the linked sprite collection gets reset to off. I've attached an image that shows what the settings look like immediately after clicking "commit".
I have not tested this with other textures with other settings. I suspect it doesn't have anything to do with being a normal map, or a linked atlas... but I don't know that. I also have only tested with Unity 4.6.0. So this could be a problem with Unity 4.6. A quick look at your source seems to show mipmap settings, but before I look deeper I thought I mention this to see if it is a known issue.
--edit--
Not sure you you allow image attachments. They are attached to this post in the editor, but I can't see them when viewing the post.